Acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy, accounting for greater than 25% of all childhood cancers (Li et al., “Cancer Incidence Among Children and Adolescents in the United States, 2001-2003,” Pediatrics 121:e1470-7 (2008)). Cure rates for ALL have improved dramatically over the past four decades with the development of risk stratification protocols that tailor therapy based on predicted risk of relapse factors, resulting in an overall five year event-free survival now approaching 80% (Escherich et al., “Cooperative Study Group for Childhood Acute Lymphoblastic Leukaemia (COALL): Long-Term Results of Trials 82, 85, 89, 92 and 97,” Leukemia 24:298-308 (2010) and Gaynon et al., “Long-Term Results of the Children's Cancer Group Studies for Childhood Acute Lymphoblastic Leukemia 1983-2002: A Children's Oncology Group Report,” Leukemia 24:285-97 (2010)). Despite these improvements, up to 20% of patients experience disease recurrence (Pui & Evans, “Treatment of Acute Lymphoblastic Leukemia,” N. Engl. J. Med. 354:166-78 (2006)). The prognosis for these children is dismal (Chessells et al., “Long-Term Follow-Up of Relapsed Childhood Acute Lymphoblastic Leukaemia,” Br. J. Haematol. 123:396-405 (2003)), even with aggressive retrieval strategies involving allogeneic stem cell transplant (Eapen et al., “Outcomes After HLA-Matched Sibling Transplantation or Chemotherapy in Children with B-Precursor Acute Lymphoblastic Leukemia in a Second Remission: A Collaborative Study of the Children's Oncology Group and the Center for International Blood and Marrow Transplant Research,” Blood 107:4961-7 (2006) and Gaynon et al., “Bone Marrow Transplantation Versus Prolonged Intensive Chemotherapy for Children with Acute Lymphoblastic Leukemia and an Initial Bone Marrow Relapse Within 12 Months of the Completion of Primary Therapy: Children's Oncology Group study CCG-1941,” J. Clin. Oncol. 24:3150-6 (2006)), and relapsed ALL remains one of the leading causes of mortality for all childhood malignancies.
Differences in gene expression, copy number, and methylation that have evolved with therapy have been profiled to determine biological pathways responsible for treatment failure. These results indicate that a number of pathways are implicated in ALL relapse (Mullighan et al., “CREBBP Mutations in Relapsed Acute Lymphoblastic Leukaemia,” Nature 471:235-9 (2011); Mullighan et al., “Genomic Analysis of the Clonal Origins of Relapsed Acute Lymphoblastic Leukemia,” Science 322:1377-80 (2008); and Hogan et al., “Integrated Genomic Analysis of Relapsed Childhood Acute Lymphoblastic Leukemia Reveals Therapeutic Strategies,” Blood 118(19):5218-26 (2011)). However the evolution of ALL clones has not been analyzed on a whole transcriptome level.
The present invention is directed to overcoming these and other deficiencies in the art.